Re: [lammps-users] Changing boundary conditions in polymer

From:

Rajesh <creativeidleminds@...24...>

Date:

Mon, 4 Dec 2017 08:25:42 +0530

Dear Axel

Thank you for your quick response. Actually initial structure was prepared using some other software and that software does not go give other option than p p p. So, no choice than to start with p p p. Can owrap command in pizza.py accomplish this or any command in vmd?

before you can change boundaries from periodic to non-periodic without breaking bonds, you have to make certain, that are are no bonds crossing periodic boundaries. as simple as that. in other words, you first have to "disentangle" your system, so that all atoms are inside the same periodic image. for example, you can try to increase your box in that dimension (without changing atom positions) until there is a sufficient separation between the periodic images.

that said, it is probably simpler to start your simulation with s p p boundaries from the very beginning, or when you are using p p p, then you need to insert some kind of barrier that prevents crossings. what is the reason to do a fully periodic simulation first?

I am simulating polyethylene with initial p p p conditions and want to change the conditions to s p p. But when I do this, polymer chains at boundary have broken bonds due to change in boundary conditions. Is there any way in lammps so that whole polymer chain can be confined in in simulation box so that no bonds are broken at boundary?